Direct observation of stepwise movement of a synthetic molecular transporter

Abstract

Controlled motion at the nanoscale can be achieved by using Watson-Crick base-pairing to direct the assembly and operation of a molecular transport system consisting of a track, a motor 1-12 and fuel [13][14][15] , all made from DNA. Here, we assemble a 100-nm-long DNA track on a two-dimensional scaffold 16 , and show that a DNA motor loaded at one end of the track moves autonomously and at a constant average speed along the full length of the track, a journey comprising 16 consecutive steps for the motor. Real-time atomic force microscopy allows direct observation of individual steps of a single motor, revealing mechanistic details of its operation. This precisely controlled, long-range transport could lead to the development of systems that could be programmed and routed by instructions encoded in the nucleotide sequences of the track and motor. Such systems might be used to create molecular assembly lines modelled on the ribosome.An effective linear molecular motor must traverse its track without dissociating [1][2][3][4][5][6][7]10,12 and run unidirectionally without external intervention [4][5][6][7][8][9][10][11][12] . Directionality may be imposed by the sequential addition of DNA instructions 1-3 or, for autonomous motors, by modifying the track sites that have been visited 5,6,12 , by coupling motion to a unidirectional reaction cycle 4,9,12 or by coordinating the conformation changes of different parts of the motor 11,12 . DNA motors that satisfy all these criteria have typically been demonstrated on tracks that allow only 1-3 steps, although a stochastic DNA 'spider' with many legs has been shown to move longer distances by biased diffusion 17 along a 100 nm track 18 .We have investigated the motion of a simple directional and processive motor fuelled by DNA hydrolysis 6 along an extended track consisting of a one-dimensional array of single-stranded attachment sites (stators), separated by 6 nm. An extended track of 15 identical stators, flanked with special start and stop stators 6 , was assembled on a rectangular DNA origami tile measuring 100 nm × 70 nm (ref. 16; Fig. 1, Supplementary Figs S1, S2). The tile comprises a 7,249-nucleotide (nt) single-stranded DNA template (genome of bacteriophage M13) hybridized to short synthetic staple strands such that the final tile consists of a raft of 24 parallel double helices tethered by the crossover of staples. Two tile designs were used. The helices of tile type A are crosslinked at 16 bp intervals, creating slight underwinding (10.7 bp per turn), which is expected to lead to a global right-handed twisting of the tile 19 . Tile type B is designed to reduce this twist: the average distance between crossovers is 15.6 bp (giving 10.4 bp per turn). The centre and ends of each staple are positioned on opposite surfaces of the tile. Selected staples were extended to include either the 22-nt stator sequence at the 5 ′ end or a hairpin at the centre 16 (Fig. 1a). Stators hybridized to complementary motor strands are visible in atomic force microscope (AFM) images...

High-speed atomic force microscopy coming of age

“…Various planned structures can be actually constructed by rationally designing base sequences of DNA. This technique has been used to prepare DNA origamis [89,107,117], capsules [110], and nanorobots [118]. Here, a study on dynamic imaging of a nanorobot is taken up.…”

“…Dynamic imaging was conducted for a DNA nanorobot in the collaboration between Hiroshi Sugiyama's group and Andrew Turberfield's group [118]. Before this study, several types of DNA nanorobots with or without an autonomous motility and processivity have been synthesized including bipedal walkers and rotary gears [185,186].…”

“…Typical examples of this class are the studies on unidirectional translocation of cellulase along cellulose fibers [83,115] and transportation of synthetic DNA motor along a series of DNA stators [118]. The study on translocation of EcoRII restriction enzyme along DNA [74] also belongs to this class.…”

Computing Cumulative Rewards Using Fast Adaptive Uniformisation

“…We consider models of DNA walkers [22], which can also be used to design logic circuits on the nanoscale. The main difference from DSD designs is that a DNA walker operates on a track of DNA strands (called anchorages) tethered to a surface, rather than in solution, and thus the model has to incorporate spatial information.…”

DNA walker circuits: computational potential, design, and verification

“…by theirs, but we consider another setting which also exhibits localised reactions: DNA walker systems [2,7,10,[14][15][16].…”